James O. McInerney

CRAIC provides tools to inspect and curate multiple sequence alignment uncertainty using posterior probabilities from pair-HMM models.

The paper introduces synteny-aware pangenome graphs to visualize genomic variation in marine bacteria, revealing structured continua of variability across genomes.

This study shows that ribosome specialisation in eukaryotes arises through constructive neutral evolution, not adaptation or selection.

This paper trains species-specific transformer models for bacterial genomic surveillance, showing they can cluster genomes, identify emerging lineages, and predict antibiotic resistance gene uptake.

This paper introduces panDecay, a software tool that unifies decay index calculations across different phylogenetic frameworks to assess branch support.

The paper identifies gene co-occurrence patterns in bacterial genomes that reveal fitness trade-offs constraining resistance mechanisms, showing species-specific gene combination rules.

The paper shows that placental phenotypes in mammals can be predicted from miRNA repertoires with high accuracy, revealing constrained genetic pathways for convergent evolution.